Article Figures & Data

Figures

Plots of similarity (generated by SimPlot) of a set of reference sequences to the 93IN999 (upper panel) and 95IN21301 (lower panel) genomes. Each curve is a comparison between the genome being analyzed and a reference genome. Each point plotted is the percent identity within a sliding window 600 bp wide centered on the position plotted, with a step size between points of 20 bp. Positions containing gaps were excluded from the comparison. The horizontal bars above the curves are a cartoon of the open reading frames of the HIV-1 genome, arranged as indicated in Fig. 3. The colors are consistent with those used for the similarity curves and indicate the subtype to which that part of the genome is most similar based on the adjacent similarity plot. Results for the remaining four genomes discussed in this report were consistent with those for 93IN999.

(A) Similarity plot as in Fig. 1 for the envgene of isolate 95IN21301, with a window size of 200 bp and a step size of 10 bp. The subtype reference sequences were majority (50%) consensus sequences for each of the subtypes, obtained from the Los Alamos web site (http://hiv-web.lanl.gov
). The dashed regions indicate areas in V1 and V2 in which less than 50% of the sites could be compared due to gaps or lack of subtype consensus. Dotted vertical lines indicate breakpoints identified by maximization of χ2 as described in Materials and Methods, with numbers of informative sites shared by 95IN21301 and the subtype in each bounded region indicated below in the color assigned to that subtype.P values were calculated by using Fisher’s exact test. Four-member trees consistent with these sites are shown at the left. Above are phylogenetic trees for each region bounded by the recombination breakpoints showing the proportion of 100 bootstrapped trees surrounding the indicated relationship. The predicted gp120/gp41 processing site is at base 2044 in this alignment. (B) Similarity plot as in panel A for the nef gene and the U3/R LTR region of isolate 95IN21301. The LTR begins at position 296 in this alignment, and the nef termination codon is at position 634. Subtype majority consensus sequences were determined by using SF170, U455, and UG037 (subtype A), RF, MN, and TH475 (subtype B), and C2220, BR025, 93IN904, 93IN905, 93IN999, 94IN11246, and 95IN21068 (subtype C).

Phylogenetic tree based on the env gene sequences compared in the HMA reaction used to identify genotypes. The tree is based on 834 sites that remained after gap stripping of the alignment predicted for the ED5 to ED12 PCR product. Numbers at nodes indicate clades supported in more than 50 of 100 bootstrapped trees, and the scale for genetic distance is indicated below. The prototype sequences for the subtypes indicated were as follows: A1, RW020; A3, SF170; C1, MA959; C2, ZAM18; C3, IN868; and C4, BR025.

Distributions of amino acid sequence differences in epitopes (A) and overall gene sequences (B). All differences in sequences are shown on the left, while only nonconservative differences identified based on physicochemical properties are shown on the right.

↵a The data are the numbers of epitope sequences among the six Indian HIV-1 isolates having predicted amino acid sequences which are identical (identical), different by only conservative amino acid changes (conservative), or different by at least one nonconservative amino acid change (nonconservative).